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Escherichia coli (E. coli) Is a Model Bacterium
FIGURE 2.13 GramNegative and GramPositive Bacteria
Gram-negative bacteria have an
extra membrane surrounding the
E. coli is a gram-negative bacterium, which means that it possesses two membranes. Outside the cytoplasmic membrane possessed by all cells are the cell wall and
a second, outer membrane (Fig. 2.13). (Although gram-negative bacteria do have two
compartments, they are nonetheless genuine prokaryotes, as their chromosome is in
the same compartment as the ribosomes and other metabolic machinery. They do not
have a nucleus, the key characteristic of a eukaryote). The presence of an outer
membrane provides an extra layer of protection to the bacteria. However, it can be
inconvenient to the biotechnologist who wishes to manufacture genetically engineered
proteins from genes cloned into E. coli. The outer membrane hinders protein secretion. Consequently there has been a recent upsurge of interest in gram-positive
bacteria, such as Bacillus, which lack the outer membrane.
Where Are Bacteria Found in Nature?
Familiar animals and plants
are vastly outnumbered by
microorganisms, in every
Bacteria are found almost everywhere. Bacteria have been found 40 miles high in the
atmosphere and seven miles deep beneath the ocean ﬂoor. Some bacteria live in the
sea, others live in fresh water, and others are found growing happily in sewage. Some
bacteria live in the soil, some are found living in the roots of plants, and some live
inside animals. Most of the bacteria that live inside animals are harmless, and some are
even of positive value in aiding digestion or synthesizing vitamins that are absorbed
by their host animal.
The total number of bacteria on our planet is estimated at an unbelievable 5 ¥
1030. Over 90% are in the soil and subsurface layers below the oceans. The total amount
of bacterial carbon is 5 ¥ 1017 grams, nearly equal to the total amount of carbon found
in plants. Probably over half of the living matter on Earth is microbial.
In addition to the “normal” habitats, some bacteria live in extreme environments
where most other life forms cannot survive. Some bacteria can live in very concentrated salt solutions, such as the Dead Sea and the Great Salt Lake. Antarctic lakes
that only thaw for a short period of each year contain bacteria. Other bacteria inhabit
hot sulfur springs, where temperatures approach boiling point and the pH is close to
1. Bacteria even grow in some thermal deep sea vents where the temperature is above
100°C and the high pressure keeps the water liquid. Bacteria from these habitats may
gram-negative bacterium Type of bacterium that has both an inner (cytoplasmic) membrane plus an outer membrane which is located outside
the cell wall
gram-positive bacterium Type of bacterium that has only an inner (cytoplasmic) membrane and lacks an outer membrane
atients are usually given antibiotics to treat bacterial infections. These are
chemical substances capable of killing most bacteria by inhibiting speciﬁc
biochemical processes, but which are relatively harmless to people. The most
commonly used antibiotics, the penicillins and cephalosporins, are synthesized by
a kind of fungus known as mold (see Fig. 2.14). However, many antibiotics are
made by one kind of bacteria in order to kill other types of bacteria. The Streptomyces group of soil bacteria produces a wide range of antibiotics including
streptomycin, kanamycin and neomycin. Some antibiotics, like chloramphenicol,
were originally made by molds but nowadays can be chemically synthesized.
Finally, some antibiotics, such as sulfonamides, are entirely artiﬁcial and are only
synthesized by chemical corporations.
Mold naturally grows
Bacterial Growth Is Suppressed by Bread Mold
The blue mold that often grows on bread makes penicillin. When penicillin is produced by
molds grown on agar in a Petri dish, it will diffuse outwards and suppress the growth of
bacteria in a circle around it.
provide products that are useful because of their resistance to extreme conditions.
Thermus aquaticus, a bacterium from hot springs, has provided the heat stable DNA
polymerase needed for the polymerase chain reaction (PCR), a widely used technique
(see Ch. 23).
When different bacteria compete to live in the same habitat, they often resort to
biological warfare. Some bacterial strains secrete toxic chemicals in order to kill off
others that are competing for the same resources. Certain bacteria synthesize toxic proteins, known as bacteriocins. These proteins are designed to kill closely related bacterial strains, yet are harmless to the producer strain. Nisin, a bacteriocin produced by
some strains of Lactococcus lactis acts as a food preservative and kills food-borne
pathogens including Listeria monocytogenes and Staphylococcus aureus. Nisin and
related bacteriocins are relatively short peptides of molecular weight 3.5 kDa. They
are formed naturally by the strains of Lactococcus that are used to make silages and
fermented foods such as wara, a Nigerian cheese product, and kimchi (Korean traditional fermented vegetables). Although scientists have found relatively few practical
applications for bacteriocins, the plasmids which carry the genes for bacteriocins have
provided the most widely used vectors for carrying genes in genetic engineering
(described in Ch. 22).
Streptomycin and related antibiotics are also made by bacteria, especially those
of the Streptomyces group, to kill competing bacteria in the soil environment. These
antibiotics are not proteins (unlike the colicins) and have been widely used clinically.
antibiotics Chemical substances that inhibit speciﬁc biochemical processes and thereby stop bacterial growth selectively; that is, without killing
the patient too.
bacteriocin A toxic protein made by bacteria to kill other, closely related, bacteria
DNA polymerase An enzyme that elongates strands of DNA, especially when chromosomes are being replicated
penicillin An antibiotic made by a mold called Penicillium, which grows on bread producing a blue layer of fungus
PCR See polymerase chain reaction
vector (a) In molecular biology a vector is molecule of DNA which can replicate and is used to carry cloned genes or DNA fragments; (b) in
general biology a vector is an organism (such as a mosquito) that carries and distributes a disease-causing microorganisms (such as yellow fever
FIGURE 2.15 A Eukaryote
Has Multiple Cell
False color transmission electron
micrograph of a plasma cell from
bone marrow. Multiple
compartments surrounded by
membranes, including a nucleus,
are found in eukaryotic cells.
Characteristic of plasma cells is the
arrangement of heterochromatin
(orange) in the nucleus, where it
adheres to the inner nuclear
membrane. Also typical is the
network of rough endoplasmic
reticulum (yellow dotted lines) in the
cytoplasm. The oval or rounded
crimson structures in the cytoplasm
are mitochondria. Magniﬁcation
¥4,500. Provided by Dr. Gopal
Murti, Science Photo Library.
Some Bacteria Cause Infectious Disease,
but Most Are Beneﬁcial
If higher organisms
disappeared from the Earth,
the prokaryotes would survive
and evolve. They do not need
us although we need them.
Bacteria are best known to the layman for causing infectious disease. Cholera, tuberculosis, bubonic plague (“Black Death”), anthrax, syphilis, gonorrhea, whooping cough,
diphtheria and a variety of other diseases are caused by bacteria. These diseases were
widespread before modern technology and hygiene largely eliminated them from
advanced societies. This was mostly due to clean water, sewers, ﬂush toilets and soap,
rather than speciﬁcally “medical” advances such as the use of antibiotics or vaccinations.
Only a small proportion of bacteria causes disease. Many bacteria help maintain
the ecosystem by degrading waste materials. For example, soil bacteria degrade the
remains of dead plants and animals and take part in the breakdown of animal waste.
Bacteria also degrade many man-made chemicals and pollutants. If “good” bacteria
did not maintain the environment, higher life-forms could not survive.
Very occasionally bacteria which are even tinier than usual infect other, larger bacteria. This results in a bacterial disease of bacteria! The best known example of this is
Bdellovibrio bacterivorus. This penetrates the outer membrane of a wide range of
gram-negative bacteria, including E. coli, Pseudomonas, etc., and takes up residence in
the space between the inner and outer membranes. Bdellovibrio lives on nutrients it
steals from the host cell. After a few hours, the host cell bursts and releases half a dozen
new Bdellovibrio cells.
Eukaryotic Cells Are Sub-Divided into Compartments
A eukaryotic cell has its genome inside a separate compartment, the nucleus. In fact,
eukaryotic cells have multiple internal cell compartments surrounded by membranes
(Fig 2.15). The nucleus itself is surrounded by a double membrane, the nuclear envenuclear envelope
Envelope consisting of two concentric membranes that surrounds the nucleus of eukaryotic cells
A mitochondrion is surrounded by two concentric membranes. The inner membrane is folded inward
to form cristae. These are the site of the respiratory chain that generates energy for the cell.
Life is modular. Complex
organisms are subdivided into
organs. Large and complex
cells are divided into
lope, which separates the nucleus from the cytoplasm, but allows some communication
with the cytoplasm via nuclear pores (Fig 2.15). The genome of eukaryotes consists of
10,000–50,000 genes carried on several chromosomes. Eukaryotic chromosomes are
linear, unlike the circular chromosomes of bacteria. Most eukaryotes are diploid, with
two copies of each chromosome. Consequently, they possess at least two copies of each
gene. In fact, eukaryotic cells often have multiple copies of certain genes as the result
of gene duplication.
Eukaryotes possess a variety of other membranes and organelles. Organelles are
subcellular structures that carry out speciﬁc tasks. Some are separated from the rest of
the cell by membranes (so-called membrane-bound organelles) but others (e.g., the
ribosome) are not. The endoplasmic reticulum is a membrane system that is continuous with the nuclear envelope and permeates the cytoplasm. The Golgi apparatus is a
stack of ﬂattened membrane sacs and associated vesicles that is involved in secretion
of proteins, or other materials, to the outside of the cell. Lysosomes are membranebound structures specialized for digestion, containing degradative enzymes.
All except a very few eukaryotes contain mitochondria (singular, mitochondrion;
Fig. 2.16). These are generally rod-shaped organelles, bounded by a double membrane.
They resemble bacteria in their overall size and shape. As will be discussed in more
detail (see Ch. 20), it is thought that mitochondria are indeed evolved from bacteria
that took up residence in the primeval ancestor of eukaryotic cells. Like bacteria, mitochondria each contain a circular molecule of DNA. The mitochondrial genome is
similar to a bacterial chromosome, though much smaller. The mitochondrial DNA has
some genes needed for mitochondrial function.
Mitochondria are specialized for generating energy by respiration and are found
in all eukaryotes. (A few eukaryotes are known that cannot respire; nonetheless these
retain remnant mitochondrial organelles—see below.) In eukaryotes, the enzymes of
respiration are located on the inner mitochondrial membrane, which has numerous
infoldings to create more membrane area. This contrasts with bacteria, where the respiratory chain is located in the cytoplasmic membrane, as no mitochondria are present.
crista (plural cristae) Infolding of the photosynthetic membrane in chloroplast
endoplasmic reticulum Internal system of membranes found in eukaryotic cells
Golgi apparatus A membrane bound organelle that takes part in export of materials from eukaryotic cells
lysosome A membrane bound organelle of eukaryotic cells that contains degradative enzymes
membrane-bound organelles Organelles that are separated from the rest of the cytoplasm by membranes
mitochondrion Membrane-bound organelle found in eukaryotic cells that produces energy by respiration
nuclear pore Pore in the nuclear membrane through which the nucleus communicates with the cytoplasm
organelle Subcellular structure that carries out a speciﬁc task. Membrane-bound organelles are separated from the rest of the cytoplasm by membranes but other organelles such as the ribosome are not.
The chloroplast is bound by a
double membrane and contains
infolded stacks of membrane
specialized for photosynthesis. The
chloroplast also contains ribosomes
Chloroplasts are membrane-bound organelles specialized for photosynthesis
(Fig. 2.17). They are found only in plants and some single-celled eukaryotes. They are
oval to rod shaped and contain complex stacks of internal membranes that contain the
green, light-absorbing pigment chlorophyll and other components needed for trapping
light energy. Like mitochondria, chloroplasts contain a circular DNA molecule and are
thought to have evolved from a photosynthetic bacterium.
The Diversity of Eukaryotes
Unlike prokaryotes that fall into two distinct genetic lineages (the eubacteria and
archaebacteria), all eukaryotes are genetically related, in the sense of being ultimately
derived from the same ancestor. Perhaps this is not surprising since all eukaryotes
share many advanced features that the prokaryotes lack.When it is said that all eukaryotes are genetically related, it is in reference to the nuclear part of the eukaryotic
genome, not the mitochondrial or chloroplast DNA molecules that have become part
of the modern eukaryotic cell.
A wide variety of eukaryotes live as microscopic single cells. However, most
eukaryotes are larger multicellular organisms that are visible to the naked eye. Traditionally, these higher organisms have been divided into the plant, fungus and animal
kingdoms.This classiﬁcation still holds, provided one remembers to include several new
groups to account for the single-celled eukaryotes. Some single-celled eukaryotes may
be viewed as plants, fungi or animals. Others are intermediate or possess a mixture of
properties and need their own miniature kingdoms.
Eukaryotes Possess Two Basic Cell Lineages
The most primitive multicellular organisms are merely aggregates of more or less identical cells. However, most multicellular organisms consist of distinct tissues and organs
containing a variety of specialized cells. Furthermore, most cells in higher organisms
do not contribute to the next generation, but die when the multicellular individual of
whom they are part dies. These are known as somatic cells (Fig. 2.20). Only the germ
line cells take part in forming a new individual. This, of course, complicates genetic
analysis. Although all cells in any multicellular organism start with an identical copy
of the genome, they differentiate to give quite different structures that perform different functions. Understanding development is a major challenge facing molecular
biology today. In animals there is a sharp division between somatic cells and germ line
cells that persists throughout the life cycle. However, plants do not set aside special
germ cells until close to the time that gametes are made.
germ line cells Reproductive cells producing eggs or sperm that take part in forming the next generation
chlorophyll Green pigment that absorbs light during photosynthesis
somatic cells Cells making up the body but which are not part of the germ cell line.
The Symbiotic Theory of Organelle Origins
branched off from the ancestral eukaryote before it
had captured the bacterium that gave rise to the mitochondrion. More recently, it was suggested that the
ancestors to these organisms did originally possess
mitochondria, but lost them secondarily during the
course of evolution. However, recent work has shown
that even Entamoeba and Giardia retain small remnant
organelles (“mitosomes”) corresponding to mitochondria. Although the capability for respiration has indeed
been completely lost, the remnant organelles function
in assembling the iron sulfur clusters found in several
well accepted theory of mitochondrial (and
chloroplast) origin is that certain bacteria were
ingested by ancestral eukaryotes and have lived in a
symbiotic relationship with their descendents ever
since. Figure 2.18 suggests how this could have
occurred. The mitochondrion contains DNA and ribosomes. The DNA of the mitochondria more closely
resembles that of bacteria than of eukaryotes.
Certain primitive single-celled eukaryotes, such as
Entamoeba and Giardia, lack the ability to respire and
instead live by fermentation (Fig. 2.19). It was once
believed that they lacked mitochondria and had
inside cell membrane
Symbiosis with Respiring Bacteria Gives Rise to the Primitive
The ancestor to the eukaryote, or “urkaryote” engulfs a respiring bacterium by surrounding it with an
infolding of the cell membrane. Consequently there is now a double membrane around the newly
enveloped bacterium. The symbiont, now called a “mitochondrion”, divides by ﬁssion like a
bacterium and provides energy for the primitive eukaryote. The mitochondrion develops infoldings of
the inner membrane that increase its energy producing capacity.
Entamoeba A very primitive single-celled eukaryote that lacks mitochondria
fermentation A biochemical process that releases energy without oxygen or light
Giardia A very primitive single-celled eukaryote that lacks mitochondria
FIGURE 2.19 Entamoeba: an Anaerobic Eukaryote
Some single-celled eukaryotes lack true respiratory mitochondria and must grow by fermentation. Shown
here is a false-color transmission electron micrograph of Entamoeba histolytica, a parasitic amoeba, which
is ingesting human red blood cells (green ovals). The white/green oval (at left) with a blue and pink central
circular area is the nucleus. Entamoeba invades and destroys the tissues of the intestines, causing amoebic
dysentery. It may spread to the liver causing abscesses to develop. The infection is acquired through
contamination of food or water or through the agency of ﬂies. Magniﬁcation: ¥830. Courtesy of: London
School of Hygiene & Tropical Medicine, Science Photo Library.
Organisms Are Classiﬁed
attempts to impose a
convenient ﬁling system upon
organisms related by
Living organisms have two names, both printed in italics; for example, Escherichia coli or
Saccharomyces cerevisiae. The ﬁrst name refers to the genus (plural, genera), a group of
closely related species.After its ﬁrst use in a publication,the genus name is often abbreviated to a single letter, as in “E. coli.” Next comes the species, or individual, name. The
genus and species are the smallest subdivision of the system of biological classiﬁcation.
Classiﬁcation of living organisms facilitates the understanding of their origins and the
relationships of their structure and function. The highest level of classiﬁcation is the
domain. There are considered to be three domains:
1. Eubacteria These are prokaryotic cells (traditional bacteria). Interestingly, this
group includes the genomes of mitochondria and chloroplasts that have been
symbiotically related to eukaryotes.
2. Archaebacteria: From a structural viewpoint, these are prokaryotes like eubacteria in that they lack a nucleus. However, their gene sequences and other biochemical features indicate they are, if anything, slightly more closely related
genetically to eukaryotes than to eubacteria.
3. Eukaryotes: Higher organisms whose DNA is carried on several chromosomes
which are found inside the nucleus. Their cells are divided into separate compartments and usually contain other organelles in addition to the nucleus.
Eukaryotes are divided into four kingdoms:
Protoctista—An accumulation of primitive, mostly single-celled eukaryotes
often referred to as protists that don’t belong to the other three main kingdoms.
There are several groups that are distinct enough that some scientists would
elevate them in rank to miniature kingdoms.
domain (of life) Highest ranking group into which living creatures are divided, based on the most fundamental genetic properties
genus A group of closely related species
kingdom Major subdivision of eukaryotic organisms, in particular the plant, fungus and animal kingdoms
Destined to form
egg or sperm
Lives no longer
Somatic Cells versus Germ Line
After an egg is fertilized and begins its development into an animal embryo, cells have two fates. A
small number of cells form the germ line, which gives rise to the gametes (eggs or sperm) that give
rise to future generations. However, most cells are part of the somatic cell line, which forms the
remainder of the organism. These somatic cells will die either before the organism as a whole, or with
it, as part of the natural life cycle.
Plants—Possess both mitochondria and chloroplasts and are photosynthetic.
Typically they are non-mobile and have rigid cell walls made of cellulose.
Fungi—Possess mitochondria but lack chloroplasts. Once thought to be plants
that had lost their chloroplasts, it is now thought they never had them. Their
nourishment comes from decaying biomatter. Although fungi are non-mobile,
they lack cellulose and their cell walls are made of chitin. They may be more
closely related to animals than plants.
Animals—Lack chloroplasts but possess mitochondria. Differ from fungi and
plants in lacking a rigid cell wall. Typically mobile. They are divided into 20 to
30 phyla (singular, phylum), depending somewhat on personal taste. Some phyla
Cnidaria—sea anemones and jellyﬁsh
Arthropoda—insects, crustaceans, etc.
Annelida—segmented worms, such as earthworms
Mollusca—snails, squids, etc.
phylum (plural phyla) Major groups into which animals are divided, roughly equivalent in rank to the divisions of plants or bacteria
Echinodermata—starﬁsh, sea urchins
Chordata—vertebrates and their relatives.
Phyla are divided into classes, such as mammals.
Classes are divided into orders, such as primates.
Orders are divided into families, such as hominids.
Families are divided into genera, such as Homo.
Genera are divided into species, such as Homo sapiens
Some Widely Studied Organisms Serve as Models
Biologists have always concentrated their attention on certain living organisms, either
because they are convenient to study or are of practical importance. Inevitably,
model organisms are atypical in some respects. For example, few bacteria grow as
fast as E. coli and few mammals breed as fast as mice. Nonetheless, information
discovered in such model systems is assumed to apply also to related organisms. In practice this often proves to be true, at least to a ﬁrst approximation. As discussed above,
the basic principles of molecular biology have been investigated in simple single-celled
prokaryotes. However, to obtain knowledge that is useful in medicine and agriculture,
researchers need model organisms that are much more closely related to humans and
to crop plants, respectively. Even these models have their limitations; ultimately, human
cells and agriculturally useful animals and plants have to be studied directly.
Yeast Is a Widely Studied Single-Celled Eukaryote
Biotechnology is a new word
but not a new occupation.
Brewing and baking both use
yeast and date back to the
earliest human civilizations.
Yeast is widely used in molecular biology for many of the same reasons as bacteria. It
is the eukaryote about which most is known and the ﬁrst whose genome was
sequenced—in 1996. Yeasts are members of the fungus kingdom and are about equally
related to animals and plants. A variety of yeasts are found in nature, but the one normally used in the laboratory is brewer’s yeast, Saccharomyces cerevisiae (Fig. 2.21). This
is a single-celled eukaryote that is easy to grow in culture. Even before the age of
molecular biology, yeast was widely used as a source of material for biochemical analysis. The ﬁrst enzymatic reactions were characterized in extracts of yeast and the word
enzyme is derived from the Greek for “in yeast”.
Although it is a “higher organism”, yeast measures up quite well to the list of useful
properties that make bacteria easy to study. In addition, it is less complex genetically
than many other eukaryotes:
a. Yeast is single-celled microorganism. Like bacteria, a yeast culture consists of
many identical cells. Although larger than bacteria, yeast cells are only about a
tenth the size of the cells of higher animals.
b. Yeast has a haploid genome of about 12 Mb of DNA with about 6,000 genes,
as compared to E. coli, which has 4,000 genes, and humans, who have approximately 25,000.
c. The natural life cycle of yeast alternates between a diploid phase and a haploid
phase. Thus it is possible to grow haploid cultures of yeast, which, like bacteria,
have only a single copy of each gene, making research interpretations easy.
d. Unlike many higher organisms, yeast has relatively few of its genes—about
5%—interrupted by intervening sequences, or introns.
e. Yeast can be grown under controlled conditions in chemically deﬁned culture
medium and forms colonies on agar like bacteria.
f. Yeast grows fast, though not as fast as bacteria. The cell cycle takes approximately 90 minutes (compared to around 20 minutes for fast growing bacteria).
g. Yeast cultures can contain around 109 cells per ml of culture media, like
Colored scanning electron
micrograph (SEM) of budding yeast
cells (Saccharomyces cerevisiae).
The larger mother cells are budding
off smaller daughter cells.
Magniﬁcation: ¥4,000. Courtesy of:
Andrew Syred, Science Photo
h. Yeast can be readily stored at low temperatures.
i. Genetic analysis using recombination is much more powerful in yeast than in
higher eukaryotes. Consequently, collections of yeast strains that each have one
yeast gene deleted are available.
Yeast illustrates the genetic
characteristics of higher
organisms in a simpliﬁed
N + N
N + N
The yeast cell alternates between
haploid and diploid phases and is
capable of growth and cell division
in either phase.
Yeast may grow as diploid or haploid cells (Fig. 2.22). Both haploid and diploid
yeast cells grow by budding, rather than symmetrical cell division. In budding, a bulge,
referred to as a bud, forms on the side of the mother cell. The bud gets larger and one
of the nuclei resulting from nuclear division moves into the bud. Finally, the cross wall
develops and the new cell buds off from the mother. Especially under conditions of
nutritional deprivation, diploid yeast cells may divide by meiosis to form haploid cells,
each with a different genetic constitution. This process is analogous to the formation
of egg and sperm cells in higher eukaryotes. However, in yeast, the haploid cells appear
identical and there is no way to tell the sexes apart and so we refer to mating types.
In contrast to the haploid gametes of animals and plants, the haploid cells of yeast may
grow and divide indeﬁnitely in culture. Two haploid cells, of opposite mating types, may
fuse to form a zygote.
In its haploid phase, Saccharomyces cerevisiae has 16 chromosomes and nearly
three times as much DNA as E. coli. Despite this, it only has 1.5 times as many genes
as E. coli. Thus a substantial portion of yeast DNA apparently lacks genetic information and so is non-coding DNA. It is easier to use the haploid phase of yeast for isolating mutations and analyzing their effects. Nonetheless, the diploid phase is also
useful for studying how two alleles of the same gene interact in the same cell. Thus,
yeast can be used as a model to study the diploid state and yet take advantage of its
haploid phase for most of the genetic analysis.
A Roundworm and a Fly Are Model
“If all the matter in the universe except the nematodes were swept
away, our world would still be dimly recognizable. . .”
—N.A. Cobb, 1914
Nematodes in oceanic mud or
inland soils may all look the
same. Nonetheless, they
harbor colossal genetic
Ultimately, researchers have to study multicellular creatures. The most primitive of
these that is widely used is the roundworm, Caenorhabditis elegans. Nematodes, or
roundworms, are best known as parasites both of animals and plants. Although it is
related to the “eelworms”—nematodes that attack the roots of crop plants—C. elegans,
is a free-living and harmless soil inhabitant that lives by eating bacteria. A single acre
budding Type of cell division seen in yeasts in which a new cell forms as a bulge on the mother cell, enlarges, and ﬁnally separates
non-coding DNA DNA sequences that do not code for proteins or functional RNA molecules
False-color scanning optical
micrograph of the soil-dwelling
bisexual nematode Caenorhabditis
elegans. The round internal
structures are eggs. C. elegans is
convenient for genetic analysis
because of its tendency to
reproduce by self-fertilization. This
results in offspring that are all
identical to the parent. It takes only
three days to reach maturity and
thousands of worms can be kept on
a culture plate. Approximate
magniﬁcation: ¥80C. Courtesy of:
James King-Holmes, Science Photo
of soil in arable land may contain as many as 3,000 million nematodes belonging to
dozens of different species.
The haploid genome of Caenorhabditis elegans consists of 97 Mb of DNA carried
on six chromosomes. This is about seven times as much total DNA as in a typical yeast
genome. C. elegans has an estimated 20,000 genes and so contains a much greater proportion of non-coding DNA than lower eukaryotes such as yeast. Its genes contain an
average of 4 intervening sequences each.
The adult C. elegans is about 1 mm long and has 959 cells and the lineage of each
has been completely traced from the fertilized egg (i.e., the zygote). It is thus a useful
model for the study of animal development. In particular, apoptosis, or programmed
cell death, was ﬁrst discovered and has since been analyzed genetically using C. elegans.
Although very convenient in the special case of C. elegans, such a ﬁxed number of cells
in an adult multicellular animal is extremely rare. C. elegans, which lives about 2–3
weeks, is also used to study life span and the aging process. RNA interference, a genesilencing technique that relies on double-stranded RNA, was discovered in C. elegans
in 1998 and is now used to study gene function during development in worms and other
higher animals. RNA interference is discussed in Ch. 11.
As noted in Chapter 1, the fruit ﬂy, Drosophila melanogaster (usually called
Drosophila) was chosen for genetic analysis in the early part of the 20th century. Fruit
ﬂies live on rotten fruit and have a 2 week life cycle, during which the female lays
several hundred eggs.The adults are about 3 mm long and the eggs about 0.5 mm. Once
molecular biology came into vogue it became worthwhile to investigate Drosophila at
the molecular level, in order to take advantage of the wealth of genetic information
already available. The haploid genome has 180 Mb of DNA carried on 4 chromosomes.
Although we normally think of Drosophila as more advanced than a primitive roundworm, it has an estimated 14,000 genes—6,000 fewer than the roundworm, C. elegans.
Genes from Drosophila contain approximately 3 intervening sequences each on
average. Research on Drosophila has concentrated on cell differentiation, development, signal transduction and behavior.
Zebraﬁsh are used to Study Vertebrate Development
Danio rerio, (previously Brachydanio rerio) the zebraﬁsh, is increasingly being used as
a model for studying genetic effects in vertebrate development. Zebraﬁsh are native
to the slow freshwater streams and rice paddies of East India and Burma, including
the Ganges River. They are small, hardy ﬁsh, about an inch long that have been bred
apoptosis Programmed suicide of unwanted cells during development or to ﬁght infection